Bioimage analysis software: is there a future beyond ImageJ? Bioimage Analysis Workshop April 30–May 1, 2012 Barcelona Euro-BioImaging – Bioimage Analysis Workshop 2012, Barcelona! 1 Euro-BioImaging – Bioimage Analysis Workshop 2012, Barcelona! 1 Bioimage analysis software: is there a future beyond ImageJ? Bioimage Analysis Workshop April 30–May 1, 2012 Barcelona Euro-BioImaging – Bioimage Analysis Workshop 2012, Barcelona! 1 Preface The workshop will bring together developers and users of imaging software for the analysis of biomedical images. Its purpose is to review the state of the art and to establish requirements for future developments. The focus will be on JAVA-based open-source solutions–in particular, ImageJ–and other open architectures that facilitate the development of plugins and community-driven projects. Bioimage Analysis Workshop The program will feature a series of invited talks by software developers and researchers who have significantly contributed to the field. In addition to the presentations, there will be special slots for posters and demos as well as roundtable discussions for drafting a roadmap for future resource developments in the context of Euro Bioimaging. The workshop includes the following topics: - Description of novel open-source image-analysis software - Solutions for the analysis of biological and biomedical images Issues in parallel implementations, multidimensional data, scripting, large data - sets, distributed computating - Standardization mechanisms and accreditation of software - Benchmarking and testing - Web-based resources Luxembourg ImageJ User & Developer Conference 24-26 October 2012 - http://imagej.tudor.lu/ Organisation - Prof. Michael Unser, Ecole Polytechnique Fédérale de Lausanne (EPFL), Switzerland - Dr. Arrate Muñoz-Barrutia, Center for Applied Medical Research, Pamplona, Spain - Dr. Andreas Jahnen, CRP Henri Tudor, Luxembourg - Dr. Daniel Sage, Ecole Polytechnique Fédérale de Lausanne (EPFL), Switzerland Euro-BioImaging – Bioimage Analysis Workshop 2012, Barcelona! 2 Support - Euro-BioImaging Project http://www.eurobioimaging.eu/ - Ecole Polytechnique Fédérale de Lausanne, Biomedical Imaging Group http://bigwww.epfl.ch/ - Centre de Recherche Public Henri Tudor, Luxembourg (ImageJ Conference) http://imagejconf.tudor.lu/ - Conference IEEE ISBI 2012, Barcelona http://biomedicalimaging.org/ Euro-BioImaging – Bioimage Analysis Workshop 2012, Barcelona! 3 Contents List of posters!5 Program - Monday!6 Program - Tuesday!7 Invited Speakers!9 Ignacio Arganda-Carreras!10 Kevin Eliceiri!11 Pavi Kankaanpää !12 Michael Liebling !13 Erik Meijering!14 Jean-Christophe Olivo-Marin!15 Wayne Rasband!16 Curtis Rueden!17 Stephan Saalfeld!18 Johannes Schindelin!19 Carlos Óscar Sorzano!20 Nico Stuurman!21 Jason Swedlow!22 Philippe Thévenaz!23 Pavel Tomancak!24 ! Poster Abstracts!27! Euro-BioImaging – Bioimage Analysis Workshop 2012, Barcelona! 4 List of posters [01] Parametric Snakes in Microscopy 28 [02] Segmentation of EM Images of Neuronal Structures Using CellProfiler 29 [03] KNIP – KNIME Image Processing and Analysis 30 [04] ALIDA – Automatic Generation of User Interfaces for Data Analysis Algorithms 31 [05] BudJ – Cell Size Computation During the Cell Cycle 32 [06] WIDE – Web Image and Data Environment 33 [07] Image Analysis Tools within an Integrated Development Environment for 34 Ecological Modeling at Various Scales [08] SynapCountJ – an ImageJ Plugin to Analyze Synaptical Densities in Neurons 35 [09] ImageJ-Driven Intelligent High Content Screening 36 [10] A Generic Solution for Tile-Based Histological Image Analysis 37 [11] Developing Open Source Image Analysis Software in Plant Sciences 38 [12] CytoSurfer – Deal with Large Data Sets Generated by Image Segmentation 39 Using ImageJ [13] ImgLib2 – Concepts and Features 40 [14] Icy: One Year Old but Already Grown-Up! 41 [15] Remote Visualization, Collaborative Annotation, and Automated Analysis of 42 High-Resolution Bioimages Through Internet [16] Extending Imaris Using Java and Launching Fiji Plugins From Within Imaris 43 [17] ImageJ Tools for STED Performance Analysis 44 [18] A KNIME-Based Workflow for the Distinction of S-Phase Stages in Cells 45 Immunolabeled for PCNA Detection [19] Open-Source Software for Single-Molecule Localization Microscopy 46 [20] Endrov – An Open Source Framework for Image Processing and Analysis 47 [21] Visualization Tool for the Examination of 3D Tracking Results [22] Multiview 3D Image Tiling for OPT and SPIM Data 49 [23] Applications of Novel Cellular Diagnostics 50 [24] PureDenoise – An ImageJ Plugin for Denoising Multidimensional Fluorescence 51 Microscopy Images [25] Digital Phantoms as a Tool for Benchmarking and Testing in Cell imaging 52 [26] Graph-Cut library for Biomedical Image Analysis 53 [27] Creating Faster, More Expressive ImageJ Scripts and Plugins with Scala 54 [28] ITK Warper for Fiji 55 [29] FucciJ – Semi-Automatic Tracking of FUCCI Cells to Build Lineage Trees Based 56 on Fluorescence Images [30] TANGO – A Customizable Tool for High Throughput for Images Analysis of 57 Nuclear Signals [31] From Acapella to ImageJ 58 [32] Web-based collaborative neuronal reconstruction with CATMAID 59 [33] Improving Acquisition Skills Using Continuous Image Quality Assessment 60 [34] CUDA-based massively parallel implementation of gray-scale 61 Mathematical Morphology operations in Java [35] CellFileAnalyzer – Automatic Plant Cell File Length Estimator 62 [36] Massive Stitcher – Integrating Plugins for New Tasks 63 Euro-BioImaging – Bioimage Analysis Workshop 2012, Barcelona! 5 PROGRAM!MONDAY, APRIL 30, 2012 8:30 Registration, installation of posters 9:15 Opening (Michael Unser) 9:20 Wayne Rasband 10:00 Pavel Tomancak 10:25 Jason Swedlow 10:50 Coffee 11:20 Johannes Schindelin 11:45 Jean-Christophe Olivo-Marin 12:10 Kevin Elicieri 12:35 Curtis Rueden 13:00 Lunch 14:00 Poster / Demo 14:45 Michael Liebling 15:10 Nico Stuurman 15:35 Erik Meijering 16:00 Coffee 16:30 Philippe Thévenaz 16:55 Ignacio Arganda-Carreras 17:20 Stephan Saalfeld 17:45 Poster / Demo 18:30 Closing of the doors Euro-BioImaging – Bioimage Analysis Workshop 2012, Barcelona! 6 PROGRAM!TUESDAY, MAY 1, 2012 8:30 Poster / Demo 9:15 Opening (Michael Unser) 9:20 Carlos Óscar Sánchez Sorzano 10:00 Pavi Kankaanpää 10:25 Organisation of the discussion 10:50 Coffee! 11:20 Small group discussions 13:00 Lunch 14:00 Poster / Demo 14:45 Small group discussions Report of a spokesman 16:00 Coffee! 16:30 Round-table Synthesis Conclusion 18:30 Closing of the doors Euro-BioImaging – Bioimage Analysis Workshop 2012, Barcelona! 7 Euro-BioImaging – Bioimage Analysis Workshop 2012, Barcelona! 8 Abstracts of speaker Euro-BioImaging – Bioimage Analysis Workshop 2012, Barcelona! 9 EURO-BIOIMAGING WORKSHOP!IGNACIO ARGANDA-CARRERAS Image Registration and Segmentation Paradigms in Fiji Ignacio Arganda-Carreras Howard Hughes Medical Institute and Massachusetts Institute of Technology Seung's lab, Dept. of Brain and Cognitive Sciences, Cambridge, MA USA [email protected]! http://biocomp.cnb.csic.es/~iarganda/ Abstract Automatic image registration and segmentation tools are two of the most demanded features of any bio-imaging software. Image registration is understood as the alignment of multiple 2D or 3D images based on a simple (translation, rigid-body, afne) or not that simple (non-linear, elastic) transformation model. This search of a common coordinate system is vital in order to integrate or compare image data obtained from diferent measurements. Image segmentation involves the automatic labeling or detection of the structures of interest in our images — complete objects or often just their boundaries—, which simplifies the image representation and facilitates the posterior analysis. In that sense, Fiji has proven to be a very popular platform for bio-medical users and developers, with a very wide spectrum of state-of-the-art algorithms in both areas. The integration of such methods along with the need of a robust and straightforward workflow to deal with large data sets originated TrakEM2, one of the most powerful Fiji plugins. TrakEM2 allows the user to process the massive amount of image data (Tera byte scale) that modern microscopes produce nowadays in afordable personal desktop computers. Moreover, TrakEM2 integrates all the software pieces for volumetric reconstruction, visualization and analysis of objects from 2D sections in a very coherent and flexible way. The challenge now consists of progressively incorporating novel and more sophisticated methods and adapt them to function on such a large scale. A very representative example is the on- going integration of machine learning based segmentation algorithms using the Weka and Knime toolboxes. Biography Ph.D. on Computer Science and Electrical Engineering for the Escuela Politécnica Superior (Universidad Autónoma de Madrid). Currently, working as a postdoctoral fellow at Sebastian Seung's lab (Massachusetts Institute of Technology, USA). Prior to that, I worked during my PhD at the Ortiz-de- Solorzano lab, at the Bioimaing Group (Lawrence Berkeley National Laboratory, California, USA), the Biocomputing Unit (National Centre for Biotechnology, Madrid, Spain), the Biomedical Signal Processing group in the Escuela Politécnica Superior (Universidad Autónoma de Madrid) and collaborated with the IRB Barcelona, in the Cell & Developmental Biology group. Right after obtaining my PhD, I worked as a researcher in the Institute of Neuroinformatics (University and ETH, Zürich) and as a consultant at the Image Processing